Multiple early factors anticipate post-acute COVID-19 sequelae.

Post-acute sequelae of COVID-19 (PASC) represent an emerging global crisis. However, quantifiable risk factors for PASC and their biological associations are poorly resolved. We executed a deep multi-omic, longitudinal investigation of 309 COVID-19 patients from initial diagnosis to convalescence (2-3 months later), integrated with clinical data and patient-reported symptoms. We resolved four PASC-anticipating risk factors at the time of initial COVID-19 diagnosis: type 2 diabetes, SARS-CoV-2 RNAemia, Epstein-Barr virus viremia, and specific auto-antibodies. In patients with gastrointestinal PASC, SARS-CoV-2-specific and CMV-specific CD8+ T cells exhibited unique dynamics during recovery from COVID-19. Analysis of symptom-associated immunological signatures revealed coordinated immunity polarization into four endotypes, exhibiting divergent acute severity and PASC. We find that immunological associations between PASC factors diminish over time, leading to distinct convalescent immune states. Detectability of most PASC factors at COVID-19 diagnosis emphasizes the importance of early disease measurements for understanding emergent chronic conditions and suggests PASC treatment strategies.

Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19.

We present an integrated analysis of the clinical measurements, immune cells, and plasma multi-omics of 139 COVID-19 patients representing all levels of disease severity, from serial blood draws collected during the first week of infection following diagnosis. We identify a major shift between mild and moderate disease, at which point elevated inflammatory signaling is accompanied by the loss of specific classes of metabolites and metabolic processes. Within this stressed plasma environment at moderate disease, multiple unusual immune cell phenotypes emerge and amplify with increasing disease severity. We condensed over 120,000 immune features into a single axis to capture how different immune cell classes coordinate in response to SARS-CoV-2. This immune-response axis independently aligns with the major plasma composition changes, with clinical metrics of blood clotting, and with the sharp transition between mild and moderate disease. This study suggests that moderate disease may provide the most effective setting for therapeutic intervention.

LAG3 ectodomain structure reveals functional interfaces for ligand and antibody recognition.

The immune checkpoint receptor lymphocyte activation gene 3 protein (LAG3) inhibits T cell function upon binding to major histocompatibility complex class II (MHC class II) or fibrinogen-like protein 1 (FGL1). Despite the emergence of LAG3 as a target for next-generation immunotherapies, we have little information describing the molecular structure of the LAG3 protein or how it engages cellular ligands. Here we determined the structures of human and murine LAG3 ectodomains, revealing a dimeric assembly mediated by Ig domain 2. Epitope mapping indicates that a potent LAG3 antagonist antibody blocks interactions with MHC class II and FGL1 by binding to a flexible 'loop 2' region in LAG3 domain 1. We also defined the LAG3-FGL1 interface by mapping mutations onto structures of LAG3 and FGL1 and established that FGL1 cross-linking induces the formation of higher-order LAG3 oligomers. These insights can guide LAG3-based drug development and implicate ligand-mediated LAG3 clustering as a mechanism for disrupting T cell activation.

Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding.

TCR-signaling strength generally correlates with peptide-MHC binding affinity; however, exceptions exist. We find high-affinity, yet non-stimulatory, interactions occur with high frequency in the human T cell repertoire. Here, we studied human TCRs that are refractory to activation by pMHC ligands despite robust binding. Analysis of 3D affinity, 2D dwell time, and crystal structures of stimulatory versus non-stimulatory TCR-pMHC interactions failed to account for their different signaling outcomes. Using yeast pMHC display, we identified peptide agonists of a formerly non-responsive TCR. Single-molecule force measurements demonstrated the emergence of catch bonds in the activating TCR-pMHC interactions, correlating with exclusion of CD45 from the TCR-APC contact site. Molecular dynamics simulations of TCR-pMHC disengagement distinguished agonist from non-agonist ligands based on the acquisition of catch bonds within the TCR-pMHC interface. The isolation of catch bonds as a parameter mediating the coupling of TCR binding and signaling has important implications for TCR and antigen engineering for immunotherapy.

Deconstructing the peptide-MHC specificity of T cell recognition.

In order to survey a universe of major histocompatibility complex (MHC)-presented peptide antigens whose numbers greatly exceed the diversity of the T cell repertoire, T cell receptors (TCRs) are thought to be cross-reactive. However, the nature and extent of TCR cross-reactivity has not been conclusively measured experimentally. We developed a system to identify MHC-presented peptide ligands by combining TCR selection of highly diverse yeast-displayed peptide-MHC libraries with deep sequencing. Although we identified hundreds of peptides reactive with each of five different mouse and human TCRs, the selected peptides possessed TCR recognition motifs that bore a close resemblance to their known antigens. This structural conservation of the TCR interaction surface allowed us to exploit deep-sequencing information to computationally identify activating microbial and self-ligands for human autoimmune TCRs. The mechanistic basis of TCR cross-reactivity described here enables effective surveillance of diverse self and foreign antigens without necessitating degenerate recognition of nonhomologous peptides.

Antibodies to Interleukin-2 Elicit Selective T Cell Subset Potentiation through Distinct Conformational Mechanisms.

Interleukin-2 (IL-2) is a pleiotropic cytokine that regulates immune cell homeostasis and has been used to treat a range of disorders including cancer and autoimmune disease. IL-2 signals via interleukin-2 receptor-ß (IL-2Rß):IL-2Rγ heterodimers on cells expressing high (regulatory T cells, Treg) or low (effector cells) amounts of IL-2Rα (CD25). When complexed with IL-2, certain anti-cytokine antibodies preferentially stimulate expansion of Treg (JES6-1) or effector (S4B6) cells, offering a strategy for targeted disease therapy. We found that JES6-1 sterically blocked the IL-2:IL-2Rß and IL-2:IL-2Rγ interactions, but also allosterically lowered the IL-2:IL-2Rα affinity through a "triggered exchange" mechanism favoring IL-2Rα(hi) Treg cells, creating a positive feedback loop for IL-2Rα(hi) cell activation. Conversely, S4B6 sterically blocked the IL-2:IL-2Rα interaction, while also conformationally stabilizing the IL-2:IL-2Rß interaction, thus stimulating all IL-2-responsive immune cells, particularly IL-2Rß(hi) effector cells. These insights provide a molecular blueprint for engineering selectively potentiating therapeutic antibodies.

Systematic Review and Meta-Analysis of Salt Valproate Preventing Switch Associated with Antidepressants in Chinese Patients With Depressive Episodes.

Objective: This overview of systematic reviews (SRs) and meta-analyses aims to critically appraise the methodology and reporting quality of relevant SRs and meta-analyses with the aim of identifying whether or not the use of valproate can prevent the switch to mania associated with antidepressant treatment in Chinese patients with depressive episodes. Methods: Electronic databases China National Knowledge Infrastructure (CNKI), Chinese Scientific Journal Database (VIP database) and Wanfang Database were searched for related SRs and meta-analyses from inception to the search date within Chinese restrictions. A total of 2 reviewers independently selected SRs and meta-analyses and collected related data, and a third reviewer was introduced if any disagreement occurred during the assessment. The Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) and the US Agency for Healthcare Research and Quality (AHRQ) were employed to evaluate quality of the reporting and methodology. Results: The switch rate in the sodium valproate group by 99% and was significantly lower than in the antidepressant-only group (0% vs 5.7%; OR = 0.18; 95% CI, 0.04-0.84; Z = 2.18; P = .03). The magnesium valproate group was similar to the sodium valproate group in switch rate; the switch rate in the antidepressant group was (2.2% vs 16.92%; OR = 0.11; 95% CI, 0.03-0.39; Z = 3.47; P = .0005). The switch rate in the salt valproate combined with a selective serotonin reuptake inhibitor (SSRI) group was lower than in the SSRI group (0.51% vs 8.4%; OR = 0.15; 95% CI, 0.04-0.51; Z = 3.01; P = .003). The switch rate in the valproate combined with serotonin noradrenaline reuptake inhibitor (SNRI) group was similar to the valproate combined with SNRI group (2.3% vs 17.5%; OR = 0.12; 95% CI, 0.03-0.53; Z = 2.79; P = .05). Conclusion: Salt valproate can reduce the switch rate related to antidepressant treatment in patients with depression.

Tau accumulation triggers STAT1-dependent memory deficits by suppressing NMDA receptor expression.

Intracellular tau accumulation forming neurofibrillary tangles is hallmark pathology of Alzheimer's disease (AD), but how tau accumulation induces synapse impairment is elusive. By overexpressing human full-length wild-type tau (termed hTau) to mimic tau abnormality as seen in the brain of sporadic AD patients, we find that hTau accumulation activates JAK2 to phosphorylate STAT1 (signal transducer and activator of transcription 1) at Tyr701 leading to STAT1 dimerization, nuclear translocation, and its activation. STAT1 activation suppresses expression of N-methyl-D-aspartate receptors (NMDARs) through direct binding to the specific GAS element of GluN1, GluN2A, and GluN2B promoters, while knockdown of STAT1 by AAV-Cre in STAT1flox/flox mice or expressing dominant negative Y701F-STAT1 efficiently rescues hTau-induced suppression of NMDAR expression with amelioration of synaptic functions and memory performance. These findings indicate that hTau accumulation impairs synaptic plasticity through JAK2/STAT1-induced suppression of NMDAR expression, revealing a novel mechanism for hTau-associated synapse and memory deficits.

Revealing the specificity of regulatory T cells in murine autoimmune diabetes.

Regulatory T cells (Tregs) control organ-specific autoimmunity in a tissue antigen-specific manner, yet little is known about their specificity in a natural repertoire. In this study, we used the nonobese diabetic (NOD) mouse model of autoimmune diabetes to investigate the antigen specificity of Tregs present in the inflamed tissue, the islets of Langerhans. Compared with Tregs present in spleen and lymph node, Tregs in the islets showed evidence of antigen stimulation that correlated with higher proliferation and expression of activation markers CD103, ICOS, and TIGIT. T cell receptor (TCR) repertoire profiling demonstrated that islet Treg clonotypes are expanded in the islets, suggesting localized antigen-driven expansion in inflamed islets. To determine their specificity, we captured TCRαß pairs from islet Tregs using single-cell TCR sequencing and found direct evidence that some of these TCRs were specific for islet-derived antigens including insulin B:9-23 and proinsulin. Consistently, insulin B:9-23 tetramers readily detected insulin-specific Tregs in the islets of NOD mice. Lastly, islet Tregs from prediabetic NOD mice were effective at preventing diabetes in Treg-deficient NOD.CD28-/- recipients. These results provide a glimpse into the specificities of Tregs in a natural repertoire that are crucial for opposing the progression of autoimmune diabetes.

Quantifying the electron-donating and -accepting capacities of wastewater for evaluating and optimizing biological wastewater treatment processes.

Biological processes have been widely used for the treatment of both domestic and industrial wastewaters. In such biological processes, pollutants are converted into pollution-free substances by microorganisms through oxidation-reduction reactions. Thus, how to quantify the internal oxidation-reduction properties wastewaters and seek out targeted countermeasures is essential to understand, operate, and optimize biological wastewater treatment systems. So far, no such approach is available yet. In this work, a novel concept of electron neutralization-based evaluation is proposed to describe the internal oxidation-reduction properties of wastewater. Pollutants in wastewater are defined as electron donor substances (EDSs) or electron acceptor substances (EASs), which could give or accept electrons, respectively. With such an electron neutralization concept, several parameters, i.e., electron residual concentration (R), economy-related index (E and Er), and economical evaluation index (Y and Yr), are defined. Then, these parameters are used to evaluate the performance and economic aspects of currently applied wastewater treatment processes and even optimize systems. Three case studies demonstrate that the proposed concept could be effectively used to reduce wastewater treatment costs, assess energy recovery, and evaluate process performance. Therefore, a new, simple, and reliable methodology is established to describe the oxidation-reduction properties of wastewater and assess the biological wastewater treatment processes.

Pure laparoscopic radical resection for type IIIa hilar cholangiocarcinoma.

BACKGROUND: Pure laparoscopic radical resection of hilar cholangiocarcinoma is still a challenging procedure, in which laparoscopic lymphadenectomy, hemihepatectomy with caudate lobectomy, and hepaticojejunostomy were included [1-4]. Relative report is rare in the world up to now. Hilar cholangiocarcinoma has a poor prognosis, especially when it occurs with lymph node metastasis or vessel invasion [5, 6]. We recently had a patient who underwent a pure laparoscopic extended right hepatectomy and lymph node dissection and hepaticojejunostomy for a type IIIa hilar cholangiocarcinoma. METHODS: The tumor was 20 × 15 × 12 mm in diameter and located in the right bile duct and common hepatic duct. Radiological examination showed that hepatic artery and portal vein was not invaded. After the division and mutilation of the right hepatic artery and the right portal vein, short hepatic veins were divided and cut off with clip and ultrasound knife from the anterior face of the vena cava. Mobilization was performed after the devascularization of the right liver, followed by the transection of liver parenchymal with CUSA and ultrasound knife. Finally, left hepatic bile duct jejunum Roux-en-Y reconstruction was performed. RESULTS: This patient underwent successfully with a totally laparoscopic procedure. An extended right hepatectomy (right hemihepatectomy combined with caudate lobectomy) and complete lymph node dissection and hepaticojejunostomy were performed in this operation. The operation time was nearly 590 min, and the intraoperative blood loss was about 300 ml. No obvious complication was observed and the postoperative hospital stay was 11 days. The final diagnosis of the hilar cholangiocarcinoma with no lymph node metastasis was pT2bN0M0 stage II (American Joint Committee on Cancer, AJCC). CONCLUSIONS: Pure laparoscopic resection for hilar cholangiocarcinoma was proved safe and feasible, which enabled the patient to recover early and have an opportunity to receive chemotherapy as soon as possible. We present a video of the described procedure.

Observation of Broad d-Wave Feshbach Resonances with a Triplet Structure.

High partial-wave (l≥2) Feshbach resonance (FR) in an ultracold mixture of ^{85}Rb-^{87}Rb atoms is investigated experimentally aided by a partial-wave insensitive analytic multichannel quantum-defect theory. Two "broad" resonances from coupling between d waves in both the open and closed channels are observed and characterized. One of them shows a fully resolved triplet structure with a splitting ratio well explained by the perturbation to the closed channel due to interatomic spin-spin interaction. These tunable "broad" d-wave resonances, especially the one in the lowest-energy open channel, could find important applications in simulating d-wave coupling dominated many-body systems. In addition, we find that there is generally a time and temperature requirement, associated with tunneling through the angular momentum barrier, to establish and observe resonant coupling in nonzero partial waves.

Pentanidium- and Bisguanidinium-Catalyzed Enantioselective Alkylations Using Silylamide as Brønsted Probase.

Most asymmetric phase transfer reactions are Brønsted base reactions, and the inorganic bases used greatly influenced the profile of the reaction. Alkoxide salts are able to activate substrates with high pKa values, but background reactions are often unavoidable. On the other hand, carbonate and phosphate salts are milder, but their low basicity limits the scope of their reactions. This presents a difficult situation whereby fragile substrates such as lactone will be hydrolyzed by a stronger base but will not be activated with a weaker one. Thus, a Brønsted probase strategy is devised, in which a strong base can be generated in situ from silylamide (probase) through the use of fluoride. In this approach, the strong base produced will be transient and not be in excess, thus reducing background and side reactions. We demonstrate this strategy using pentanidinium and bisguanidinium as catalysts; highly enantioselective phase transfer alkylation of several types of substrates including dihydrocoumarin (lactone) can be achieved. We found that the probase also acts as a silylation reagent, generating silyl enol ether or silyl ketene acetal, which are key intermediates in the reaction. We further propose that hypervalent silicates form ion-pairs with pentanidinium and bisguanidinium as intermediates in the reaction, and it is through these ion-pairs that the selective enantiofacial approach of the electrophile is determined.

Diversity-oriented approaches for interrogating T-cell receptor repertoire, ligand recognition, and function.

Molecular diversity lies at the heart of adaptive immunity. T-cell receptors and peptide-major histocompatibility complex molecules utilize and rely upon an enormous degree of diversity at the levels of genetics, chemistry, and structure to engage one another and carry out their functions. This high level of diversity complicates the systematic study of important aspects of T-cell biology, but recent technical advances have allowed for the ability to study diversity in a comprehensive manner. In this review, we assess insights gained into T-cell receptor function and biology from our increasingly precise ability to assess the T-cell repertoire as a whole or to perturb individual receptors with engineered reagents. We conclude with a perspective on a new class of high-affinity, non-stimulatory peptide ligands we have recently discovered using diversity-oriented techniques that challenges notions for how we think about T-cell receptor signaling.

Multiparameter single-cell profiling of human CD4+FOXP3+ regulatory T-cell populations in homeostatic conditions and during graft-versus-host disease.

Understanding the heterogeneity of human CD4+FOXP3+ regulatory T cells (Tregs) and their potential for lineage reprogramming is of critical importance for moving Treg therapy into the clinics. Using multiparameter single-cell analysis techniques, we explored the heterogeneity and functional diversity of human Tregs in healthy donors and in patients after allogeneic hematopoietic stem cell transplantation (alloHSCT). Human Tregs displayed a level of complexity similar to conventional CD4+ effector T cells with respect to the expression of transcription factors, homing receptors and inflammatory cytokines. Single-cell profiling of the rare Treg producing interleukin-17A or interferon-γ showed an overlap of gene expression signatures of Th17 or Th1 cells and of Tregs. To assess whether Treg homeostasis is affected by an inflammatory and lymphopenic environment, we characterized the Treg compartment in patients early after alloHSCT. This analysis suggested a marked depletion of Treg with a naive phenotype in patients developing acute graft-versus-host disease, compared with tolerant patients. However, single-cell profiling showed that CD4+FOXP3+ T cells maintain the Treg gene expression signature and Treg-suppressive activity was preserved. Our study establishes that heterogeneity at the single-cell level, rather than lineage reprogramming of CD4+FOXP3+ T cells, explains the remarkable complexity and functional diversity of human Tregs.

Recent advances in clay mineral-containing nanocomposite hydrogels.

Clay mineral-containing nanocomposite hydrogels have been proven to have exceptional composition, properties, and applications, and consequently have attracted a significant amount of research effort over the past few years. The objective of this paper is to summarize and evaluate scientific advances in clay mineral-containing nanocomposite hydrogels in terms of their specific preparation, formation mechanisms, properties, and applications, and to identify the prevailing challenges and future directions in the field. The state-of-the-art of existing technologies and insights into the exfoliation of layered clay minerals, in particular montmorillonite and LAPONITE®, are discussed first. The formation and structural characteristics of polymer/clay nanocomposite hydrogels made from in situ free radical polymerization, supramolecular assembly, and freezing-thawing cycles are then examined. Studies indicate that additional hydrogen bonding, electrostatic interactions, coordination bonds, hydrophobic interaction, and even covalent bonds could occur between the clay mineral nanoplatelets and polymer chains, thereby leading to the formation of unique three-dimensional networks. Accordingly, the hydrogels exhibit exceptional optical and mechanical properties, swelling-deswelling behavior, and stimuli-responsiveness, reflecting the remarkable effects of clay minerals. With the pivotal roles of clay minerals in clay mineral-containing nanocomposite hydrogels, the nanocomposite hydrogels possess great potential as superabsorbents, drug vehicles, tissue scaffolds, wound dressing, and biosensors. Future studies should lay emphasis on the formation mechanisms with in-depth insights into interfacial interactions, the tactical functionalization of clay minerals and polymers for desired properties, and expanding of their applications.

Molecular evidence for nitrite-dependent anaerobic methane-oxidising bacteria in the Jiaojiang Estuary of the East Sea (China).

Nitrite-dependent anaerobic methane oxidation (N-DAMO) is a recently discovered process linking the global carbon and nitrogen cycles. This process was reported to be mediated by "Candidatus Methylomirabilis oxyfera". To date, M. oxyfera-like bacteria have been detected in a limited number of freshwater habitats, but whether these bacteria occur in estuarine habitats is currently unknown. In this study, the distribution, diversity and abundance of M. oxyfera-like bacteria were studied in the sediment of the Jiaojiang Estuary of the East Sea (China). Both the 16S ribosomal RNA (rRNA) and pmoA genes confirmed the occurrence of M. oxyfera-like bacteria in the examined estuary. The recovered 16S rRNA gene sequences showed 91.5-97.2 % identity to the 16S rRNA gene of M. oxyfera, and the recovered pmoA gene sequences showed 85.1-95.4 % identity to the pmoA gene of M. oxyfera. Quantitative PCR further confirmed the occurrence of M. oxyfera-like bacteria in this estuary, with the abundance varying from 5.80 ± 0.28 × 10(4) to 8.35 ± 0.52 × 10(7) copies g (dry weight)(-1). Correlation analysis indicated that the sediment organic content was the most important factor affecting the distribution of M. oxyfera-like bacterial communities in the examined sediments among the environmental factors investigated. This study demonstrated for the first time the existence of M. oxyfera-like bacteria in an estuarine environment and showed the correlations between the distribution of these bacteria and the estuarine environmental conditions.

A leveling method based on current feedback mode of scanning electrochemical microscopy.

Substrate leveling is an essential but neglected instrumental technique of scanning electrochemical microscopy (SECM). In this technical note, we provide an effective substrate leveling method based on the current feedback mode of SECM. By using an air-bearing rotary stage as the supporter of an electrolytic cell, the current feedback presents a periodic waveform signal, which can be used to characterize the levelness of the substrate. Tuning the adjusting screws of the tilt stage, substrate leveling can be completed in minutes by observing the decreased current amplitude. The obtained high-quality SECM feedback curves and images prove that this leveling technique is valuable in not only SECM studies but also electrochemical machining.

Use of tyrosinase-inorganic salt hybrid nanoflowers and tyrosinase-MOF hybrid composites for elimination of phenolic pollutants from industrial wastewaters.

Removal of phenolic pollutants from industrial wastewaters is always an important practical problem. Use of enzymes for dephenolization provides a green solution. In this work, enzymatic methods were developed by employing mushroom tyrosinase immobilized as enzyme-Cu3(PO4)2 hybrid nanoflowers and enzyme-metal organic framework (i.e., ZIF-8 and HKUST-1) hybrid composites, which were shown to be superior to processes mediated by tyrosinase immobilized on other supports in both dephenolization efficiency and reusability. Comparatively, tyrosinase@Cu3(PO4)2 and tyrosinase@HKUST-1 were better than tyrosinase@ZIF-8 in both specific activity and dephenolization efficiency. Typical phenolic pollutants, including 3 monophenols (phenol, p-cresol, p-chlorophenol) and 3 bisphenols (BPA, BPB, BPF), can be completely eliminated within 0.5-4 h. The dephenolization order was discussed based on the enzyme's substrate specificity. The operability and reusability of these hybrid biocomposites were highly improved by entrapping into alginate gels or by incorporating with modified magnetic Fe3O4 nanoparticles. Particularly, the magnetic biocatalyst was prepared via a facile one-pot/one-step de novo synthetic strategy, optimized by using response surface methodology (RSM). The as-prepared magnetic tyrosinase@mHKUST-1 retained a high dephenolization efficiency of 81% after 10 cycles and was effective for continuous dephenolization for at least 24 h. These hybrid biocomposites were also successfully applied to treatment of real industrial wastewater from a coke plant.